We are changing our user from a Mac to a Windows (7) based computer and we are running in to issues with files that she created on the Mac version of Adobe Illustrator. She used some fonts (AGaramond-BoldItalic for example) and it works great on the Mac. I copied all the font files to the windows computer and made sure they work (opened Illustrator and created a document with the fonts).

The issue now is that when we open the old documents from the Mac on the Windows computer it gives an error "Font not found on the system; missing font has been substituted."

I am not sure how to tell the file that the fonts Are there because when it opens all the fonts are to a default Arial.

So far I have tried:

Removing all Adobefnt*.lst files

Resetting adobe settings by holding ctrl+alt+shift and opening the program

There are more cache files than the adobefnt files. See here for more detailed instructions on cleaning your font caches. That said, it sounds likely that the issue is that your fonts are mac only, as Larry said above. You should be able to use Type -> Find Font... to replace them with whatever version you have on the PC but watch for formatting/flow changes. Also, my condolences to your designer. ;-)